EPIFISH
Hooking the bigger fish through epigenetics
Innovative epigenetic markers for fish domestication Project Objectives
Second generation of Nile tilapia (Oreochromis niloticus) reared in our recirculating aquaculture system at Nord University. Traditional fisherman in the river Nile.
Effective breeding strategies are crucial to the long-term sustainability of the aquaculture sector and its ability to meet the growing global demand for seafood products. We spoke to Professor Jorge Fernandes about the EPIFISH project’s work in investigating the role of epigenetics in fish domestication, which holds important implications for aquaculture biotechnology. The aquaculture industry as a whole will need to increase production in future to meet growing global demand for fish and shellfish. The ability to domesticate and selectively breed fish and shellfish is central to the sustainability of the industry, a topic at the heart of the EPIFISH project’s work. “We are looking at phenotypic changes in fish removed from the wild and taken into captivity. We are looking at these changes over three generations,” explains Professor Jorge Fernandes, the project’s Principal Investigator. This work was prompted to a large degree by earlier research which showed that selective breeding in domesticated fish could lead to large increases in size, even over relatively short timescales. “An 85 percent increase in average fish weight was recorded in Nile tilapia (Oreochromis niloticus), which would represent a huge gain for the industry. What amazed me was that this happened so quickly, over just five generations,” outlines Professor Fernandes.
EPIFISH project This rapid increase cannot be attributed solely to genetic factors, believes Professor Fernandes, and now he and his colleagues in the project are investigating the importance of epigenetics in fish domestication. Researchers are using the Nile tilapia as a model species, a fish which is commercially very important. “Nile Tilapia is the secondmost important farmed fish worldwide in terms of the volume of production, while it also has a very short generation time,
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reaching sexual maturity at the age of 4-5 months. This means we can look at several generations within the timeframe of the project,” says Professor Fernandes. The Nile tilapia itself is native to Egypt and central Africa, but it is now found across the world, in a range of different environmental conditions. “They can deal with a wide range of temperatures, tolerate different salinities, and eat pretty much anything, both animals and plants,” continues Professor Fernandes. “They do very well on very little.”
regulation. This is not only because they can be epigenetically modified themselves, they can also regulate the expression of a number of genes involved in epigenetic regulation,” outlines Professor Fernandes. A second major priority in the project is to investigate the role of DNA modifications in fish domestication. Here, Professor Fernandes and his colleagues are looking at the methylation and hydroxymethylation of cytosine bases. “We want to see what happens to the expression of these miRNAs
The hypothesis behind this project is that if we include epigenetic markers then we will be able to cover a larger proportion of phenotype variability in the traits we want – like disease resistance, growth, and age at sexual maturity The wild fish were initially collected from Egypt and taken to a research station at Nord University in Norway, where Professor Fernandes is based. Researchers are observing the domestication of these fish over several generations, with Professor Fernandes and his colleagues looking at the epigenetic markers of this process. “Epigenetic changes occur beyond the genome, or genetics, and help to regulate the differentiation of the cells and how they function,” he explains. A lot of attention in the project is focused on miRNA variants, small, non-coding RNAs that are involved in a lot of biological processes. “They are known to be important players in epigenetic
from one generation to the next in these groups, both the selected lines and the control lines. “We want to investigate how the new environmental conditions in captivity (e.g., feed, water temperature and photoperiod) affect the expression of miRNAs, and how their DNA is modified. We plan to look at whether the modifications change across generations,” says Professor Fernandes. The other comparison researchers are making is between the selected and control groups within each generation. “The idea behind this is to find out which microRNAs and DNA modifications can explain differences in size between the selected fish and the control fish,” continues Professor Fernandes. “We’re looking to see what happens to the fish during domestication, and at how this changes across generations.”
Aquaculture industry This research holds important long-term implications for the aquaculture industry and how fish are bred for the commercial market. Existing selection programmes are based on genetic factors, yet these markers do not explain all the variations that can be seen between fish of the same species. “The hypothesis behind this project is that if we include epigenetic markers then we will be able to cover a larger proportion of
when you put a wild fish in captivity,” he says. A selective breeding programme has been established at the research station, from which researchers aim to gain new insights in this respect. “We put these wild larvae that we collected from Egypt in a re-circulating aquaculture system, and monitored them as they grew,” explains Professor Fernandes. “When they reached sexual maturity we separated them into groups; one of averagely sized fish – the control lines – and another that were about 15 percent bigger – the selected lines.” The fish from this selective breeding programme were subjected to two sets of comparisons. One involves looking at changes
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phenotype variability in the traits we want – like disease resistance, growth, and age at sexual maturity,” says Professor Fernandes. Finding and validating these epigenetic markers could lead to the identification of new parameters in selective breeding, which would be enormously beneficial for the aquaculture industry, yet Professor Fernandes says this is not an immediate prospect. “A lot of fundamental research needs to be done before we get to that stage,” he acknowledges. Researchers have nevertheless made progress over the course of the project, for example in identifying differences between small and big fish in terms of miRNA expression, DNA methylation and hydroxymethylation. Professor Fernandes and his colleagues aim to establish the proof of concept in the ERC-funded Epimark project. “We will try to validate these results by looking at more fish, including fish of different sizes and ages and from different locations,” he says. In future, Professor Fernandes hopes to build further on these findings, while also pursuing more exploratory research. “If we find some promising markers, it would be sensible to continue in an applied direction, to validate them and see if we can develop them further to use in aquaculture. I plan to combine this with continued fundamental research,” he outlines. Fisherman using a trap to catch tilapia in Luxor.
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The overarching aim of EPIFISH is to ascertain the importance of epigenetics (DNA methylation and microRNAs) in fish domestication using the Nile tilapia as model species. The identification of epigenetic markers will enable the development and application of epigenomic selection as a new feature in future selective breeding programmes.
Project Funding
EPIFISH has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no 683210) and from the Research Council of Norway under the Toppforsk programme (grant agreement no 250548/F20).
Project Partners
• P rofessor John Liu, Syracuse University, USA • Professor Francesc Piferrer, CSIC, Spain • Professor Pål Sætrom, NTNU, Norway • Alex Alvarez, Genomar, Norway • Leonidas Papaharisis, Nireus, Greece
Contact Details
Project Coordinator, Jorge Manuel de Oliveira Fernandes Faculty of Biosciences and Aquaculture Nord University 8026 Bodø, Norway T: +47 75 51 77 36 E: jorge.m.fernandes@nord.no W: http://www.jmofernandes.com
Professor Jorge Fernandes
Jorge Fernandes is a Professor in Genomics and Molecular Biology at Nord University in Norway. His main research interests are domestication, antimicrobial peptides, microRNAs and the epigenetic regulation of gene networks by environmental factors. His research is aimed at commercially relevant fish species, such as nile tilapia, Atlantic cod and Atlantic halibut.
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